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1. Amino acids are organic compounds that contain an amino group and a carboxyl group. Most amino acids have an L-configuration at the alpha carbon. 2. Amino acids can be classified based on the properties of their variable side chains into four groups: nonpolar, neutral polar, acidic, and basic. 3. The ionization states and charges of amino acid functional groups depend on pH, as described by the Henderson-Hasselbalch equation. Most amino acids have an isoelectric point between pH 5-7.

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64 views9 pages

Fdafsf

1. Amino acids are organic compounds that contain an amino group and a carboxyl group. Most amino acids have an L-configuration at the alpha carbon. 2. Amino acids can be classified based on the properties of their variable side chains into four groups: nonpolar, neutral polar, acidic, and basic. 3. The ionization states and charges of amino acid functional groups depend on pH, as described by the Henderson-Hasselbalch equation. Most amino acids have an isoelectric point between pH 5-7.

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Amino Acids

Mary K. Campbell
Shawn O. Farrell
international.cengage.com/

Amino Acids and Peptides

Amino acid: a compound that contains


both an amino group and a carboxyl
group

-Amino acid has an amino group


attached to the carbon adjacent to
the carboxyl group
-carbon also bound to side chain
group, R
R gives identity to amino acid
Two steroisomers of amino acids
are designated L- or D-. Based on
similarity to glyceraldehdye

Paul D. Adams University of Arkansas

Amino Acid Structure and Properties


With the exception of glycine, all protein-derived
amino acids have at least one stereocenter (the carbon) and are chiral (stereoisomers)
the vast majority of -amino acids have the Lconfiguration at the -carbon (Proline is usually D)

Side-chain carbons in other amino acids designated


with Greek symbols, starting at a carbon (etc)
Amino acids can be referred to by three-letter or oneletter codes. Table 3.1 (KNOW THESE)

Individual Amino Acids


Group A: Nonpolar side chains- Ala, Val, Leu, Ile,
Pro. Phe, Trp, Met.
Ala, Val, Leu, Ile, Pro- contain aliphatic hydrocarbon
group. Pro has cyclic structure.

Phe- hydrocarbon aromatic ring.


Trp- Indole ring side chain, aromatic.
Met- Sulfur atom in side chain.

Amino Acids (contd)

Amino Acids (contd)

Group B: Neutral Polar side chains- Ser, Thr, Tyr,


Cys, Glu, Asn

Group C: Acidic Side Chains: Glu, Asp


Both have a carboxyl group in side chain

Ser, Thr- Side chain is polar hydroxyl group


Can lose a proton, forming a carboxylate ion
Tyr- hydroxyl group bonded to aromatic hydrocarbon
group

These amino acids are negatively charged at neutral


pH

Cys- Side chain contains thiol group (-SH)


Gln, Asn- contain amide bonds in side chain

Amino Acids (contd)


Group D: Basic side chains: His, Lys, Arg
Side chains are positively charged at pH 7

Arg-side chain is a guanidino group


His-side chain is an imidazole group
Lys-side chain NH3 group is attached to an aliphatic
hydrocarbon chain

Amino acid summary


Important structural features:
1. All 20 are -amino acids
2. For 19 of the 20, the -amino group is primary; for proline,
it is secondary
3. With the exception of glycine, the -carbon of each is a
stereocenter
4. Isoleucine and threonine contain a second stereocenter
5. 3, and 1-letter codes in Table 3.1.

Uncommon Amino Acids

Ionization of Amino Acids

Each derived from


a common amino
acid by a
modification

In amino acid,
carboxyl group (-)
and amino group
(+) are charged at
neutral pH.

hydroxylysine and
hydroxyproline are
found only in a
few connective
tissues
such as collagen
thyroxine is found
only in the thyroid
gland

In free amino
acids -carboxyl,
and a-amino
groups have
titratable protons.
Some side chains
do as well

Ionization of Amino Acids

Titration of Amino Acids

Remember, amino acids without charged groups on side chain


exist in neutral solution as zwitterions with no net charge

When an amino acid is titrated, the titration curve represents the reaction of
each functional group with the hydroxide ion

Titration of alanine with NaOH

Titration of histidine with NaOH

Acidity: -COOH Groups

Basicity

The average pKa of an -carboxyl group is 2.19,


which makes them considerably stronger acids than
acetic acid (pKa 4.76)

-NH3+ groups: The average value of pKa for an -NH3+ group


is 9.47, compared with a value of 10.76 for a 2
alkylammonium ion
Guanidine Group
The side chain of arginine is a considerably stronger base
than an aliphatic amine
basicity of the guanido group is attributed to the large
resonance stabilization of the protonated form relative to
the neutral form

the greater acidity of the amino acid carboxyl group is


due to the electron-withdrawing inductive effect of the NH3+ group

Imidazole Group
The side chain imidazole group of histidine is a
heterocyclic aromatic amine

Ionization vs pH

Ionization vs pH (contd)

Given the value of pKa of each functional group, we


can calculate the ratio of each acid to its conjugate
base as a function of pH
Consider the ionization of an -COOH

substituting the value of Ka (1 x 10-2) for the hydrogen


ion concentration at pH 7.0 (1.0 x 10-7) gives

COOH + H2 O

pKa = 2.00

COO

+ H3 O

[ H 3 O + ] [ -COO - ]
[ -COO H]

[ -COO - ]

or

[ -COO H]

[ -COO H]

Ka
+

[ H3O ]

-2
1.00 x 10

5
= 1.00 x 10

-7
1.00 x 10

writing the acid ionization constant and rearranging


terms gives (remember Ch. 2)
Ka =

[ -COO - ]

Ka
[ H 3 O+ ]

at pH 7.0, the -carboxyl group is virtually 100% in


the ionized or conjugate base form, and has a net
charge of -1
we can repeat this calculation at any pH and
determine the ratio of [-COO-] to [-COOH] and the
net charge on the -carboxyl at that pH

Ionization vs pH (contd)

Ionization vs pH

We can also calculate the ratio of acid to conjugate


base for an -NH3+ group; for this calculation,
assume a value 10.0 for pKa

substituting values for Ka of an -NH3+ group and


the hydrogen ion concentration at pH 7.0 gives
[ -NH 2 ]

NH3

+ H2 O

pKa = 10.00

NH2

+ H3 O+

writing the acid ionization constant and rearranging


gives
[ -NH 2 ]

[ -NH 3 + ]

[ -NH 3 ]
+

Ka

[H 3 O+ ]

Ka
[H 3 O+ ]

- 10
1.00 x 10

-3
= 1.00 x 10

-7
1.00 x 10

at pH 7.0, the ratio of -NH2 to -NH3 + is


approximately 1 to 1000
at this pH, an -amino group is 99.9% in the acid
or protonated form and has a charge of +1

Henderson-Hasselbalch Equation

Isoelectric pH

We have calculated the ratio of acid to conjugate


base for an -carboxyl group and an -amino group
at pH 7.0
We can do this for any weak acid and its conjugate
base at any pH using the Henderson-Hasselbalch
equation (Ch. 2)

Isoelectric pH, pI: the pH at which the majority of molecules


of a compound in solution have no net charge

pH = pK a + log

the pI for glycine, for example, falls midway between the pK a


values for the carboxyl and amino groups

[conjugate base]

pI = 1 ( p K a COOH +
2

[weak acid]

p Ka N H3 + )

= 1 (2.35 + 9.78) = 6.06


2
Isoelectric pH values for the 20 protein-derived amino acids are
given in Table 3.2

Electrophoresis
Electrophoresis: the process of separating
compounds on the basis of their electric charge
electrophoresis of amino acids can be carried out
using paper, starch, agar, certain plastics, and
cellulose acetate as solid supports
in paper electrophoresis, a paper strip saturated with
an aqueous buffer of predetermined pH serves as a
bridge between two electrode vessels

Electrophoresis: separation of polar compounds based on their


mobility through a solid support. The separation is based on
charge (pI) or molecular mass.

_ _

_
+ +

28

Peptide Bonds

Geometry of Peptide Bond

Individual amino acids


can be linked by forming
covalent bonds.
Peptide bond: the
special name given to
the amide bond between
the -carboxyl group of
one amino acid and the
-amino group of
another amino acid

the four atoms of a peptide bond and the two alpha


carbons joined to it lie in a plane with bond angles of
120about C and N
to account for this geometry, a peptide bond is most
accurately represented as a hybrid of two contributing
structures (resonance structures)
the hybrid has considerable C-N double bond
character and rotation about the peptide bond is
restricted

Resonance Structures of Peptide Bond

Peptides
peptide: the name given to a short polymer of amino
acids joined by peptide bonds; they are classified by
the number of amino acids in the chain
dipeptide: a molecule containing two amino acids
joined by a peptide bond
tripeptide: a molecule containing three amino acids
joined by peptide bonds
polypeptide: a macromolecule containing many
amino acids joined by peptide bonds
protein: a biological macromolecule of molecular
weight 5000 g/mol or greater, consisting of one or
more polypeptide chains

Peptides with Physiological Activity (contd)

Peptides with Physiological Activity

E-A-Y-L-V-C-G-E-R
F-V-N-Q-H-L-F-S-H-L-K
G-C-F-L-P-K
L-G-A

F-V-N-Q-H-L-F
S-H-L-K-E-A-Y
L-V-C-G-E-R-G-C-F
L-P-K-L-G-A

F-V-N-Q-H-L-F
F-V-N-Q-H-L-F-S-H-L-K
S-H-L-K-E-A-Y
E-A-Y-L-V-C-G-E-R
L-V-C-G-E-R-G-C-F
G-C-F-L-P-K
L-P-K-L-G-A
L-G-A
F-V-N-Q-H-L-F-S-H-L-K-E-A-Y-L-V-C-G-E-R-G-C-F-L-P-K-L-G-A
35

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